Various blender fixes and tweaks

blender/extension/__init__.py

@@ -1,4 +1,5 @@
 import bpy
+import os
 
 from .ui.import_pdb_operator import ImportPDBOperator
 from .ui.animate_trajectory_operator import AnimateTrajectoryOperator
@@ -94,7 +95,7 @@ def update_segmentation_path(self, context):
     self.ProteinRunway_segmentation_items.clear()
 
     path = self.ProteinRunway_segmentation_path
-    if len(path) == 0:
+    if len(path) == 0 or not os.path.isfile(path):
         # The path has been removed, clear out the UI lists:
         return
 

blender/extension/blender_manifest.toml

@@ -4,31 +4,18 @@ id         = "protein_runway"
 version    = "0.0.1"
 name       = "Protein Runway"
 tagline    = "Render proteins with their trajectories, segment and extract normal modes."
-maintainer = "TODO <[email protected]>"
+maintainer = "Andrew Radev <[email protected]>"
 
-type = "add-on"
-
-# # Optional: link to documentation, support, source files, etc
-# website = "https://extensions.blender.org/add-ons/my-example-package/"
-
-# # Optional: tag list defined by Blender and server, see:
-# # https://docs.blender.org/manual/en/dev/advanced/extensions/tags.html
-# tags = ["Animation", "Sequencer"]
+type    = "add-on"
+website = "https://andrewradev.github.io/protein-runway/"
+tags    = ["Animation", "Import-Export", "Physics"]
 
 blender_version_min = "4.2.0"
-# # Optional: Blender version that the extension does not support, earlier versions are supported.
-# # This can be omitted and defined later on the extensions platform if an issue is found.
-# blender_version_max = "5.1.0"
 
 # https://docs.blender.org/manual/en/dev/advanced/extensions/licenses.html
 license = [
   "SPDX:GPL-3.0-or-later",
 ]
-# # Optional: required by some licenses.
-# copyright = [
-#   "2002-2024 Developer Name",
-#   "1998 Company Name",
-# ]
 
 platforms = ["windows-x64", "macos-arm64", "linux-x64", "macos-x64"]
 # Other supported platforms: "windows-arm64"
@@ -92,33 +79,3 @@ wheels = [
   "./wheels/tqdm-4.67.1-py3-none-any.whl",
   "./wheels/waterdynamics-1.2.0-py3-none-any.whl",
 ]
-
-# # Optional: add-ons can list which resources they will require:
-# # * files (for access of any filesystem operations)
-# # * network (for internet access)
-# # * clipboard (to read and/or write the system clipboard)
-# # * camera (to capture photos and videos)
-# # * microphone (to capture audio)
-# #
-# # If using network, remember to also check `bpy.app.online_access`
-# # https://docs.blender.org/manual/en/dev/advanced/extensions/addons.html#internet-access
-# #
-# # For each permission it is important to also specify the reason why it is required.
-# # Keep this a single short sentence without a period (.) at the end.
-# # For longer explanations use the documentation or detail page.
-#
-# [permissions]
-# network = "Need to sync motion-capture data to server"
-# files = "Import/export FBX from/to disk"
-# clipboard = "Copy and paste bone transforms"
-
-# # Optional: advanced build settings.
-# # https://docs.blender.org/manual/en/dev/advanced/extensions/command_line_arguments.html#command-line-args-extension-build
-# [build]
-# # These are the default build excluded patterns.
-# # You only need to edit them if you want different options.
-# paths_exclude_pattern = [
-#   "__pycache__/",
-#   "/.git/",
-#   "/*.zip",
-# ]

blender/extension/lib/segmentation.py

@@ -2,21 +2,27 @@
 import re
 from collections import defaultdict
 
+
+class ParseError(Exception):
+    pass
+
+
 def parse_segmentation_file(path):
     """
     Expected columns: 'index', 'method', 'domain_count', 'chopping'
     """
     # A nested dictionary of { <method>: { <domain_count>: <chopping> } }
     segmentations = defaultdict(dict)
 
-    # TODO (2024-11-17) Handle errors
-
-    with open(path) as f:
-        reader = csv.DictReader(f, delimiter='\t')
-        for row in reader:
-            segmentations[row['method']][row['domain_count']] = row['chopping']
+    try:
+        with open(path) as f:
+            reader = csv.DictReader(f, delimiter='\t')
+            for row in reader:
+                segmentations[row['method']][row['domain_count']] = row['chopping']
 
-    return segmentations
+        return segmentations
+    except Exception as e:
+        raise ParseError(f"Couldn't parse segmentation file {path}") from e
 
 
 def generate_domain_ranges(chopping):
@@ -25,7 +31,7 @@ def generate_domain_ranges(chopping):
     for domain in chopping.split(','):
         regions = []
         for region in domain.split('_'):
-            if re.match('^\d+$', region) is None:
+            if re.match(r'^\d+$', region) is None:
                 start, end = region.split('-')
             else:
                 # Only a single domain

blender/extension/ui/import_pdb_operator.py

@@ -60,12 +60,6 @@ def execute(self, context):
             o.select_set(True)
         bpy.ops.protein_runway.animate_trajectory('INVOKE_DEFAULT')
 
-        # TODO (2024-11-14) This is messy and invasive, it might interfere with
-        # multiple trajectories
-        #
-        # Fit the number of global frames to this trajectory's length.
-        bpy.data.scenes[0].frame_end = len(mda_universe.trajectory)
-
         return {'FINISHED'}
 
     def draw_alpha_carbons(self, universe, domain_regions, add_convex_hull):

blender/extension/ui/import_trajectory_panel.py

@@ -8,7 +8,7 @@
 
 
 class ImportTrajectoryPanel(bpy.types.Panel):
-    bl_label       = "Import Trajectory"
+    bl_label       = "ProteinRunway: Import Trajectory"
     bl_idname      = "PROTEINRUNWAY_PT_import_panel"
     bl_space_type  = "PROPERTIES"
     bl_region_type = "WINDOW"